The World Surf League confirmed a shark sighting was the reason Wilson's heat was postponed to allow the emergency response team to collect the two surfers in the water.
There were 22 minutes to go in the semi-final when event officials received word of a shark sighting in the area.
"It's the same as what we saw earlier, a small shark, but it's inside the take-off area in the competition zone so safety first," WSL commissioner Keren Perrow said.
"Surfers are on the back of the skis, the drones are monitoring and as far as we can see it's swum out."
Wilson, 30, continued competing on Tuesday under the impossible strain of having his J-Bay trauma resurface.
The disruption didn't help him. When the heat resumed with few waves rolling in he went down to miss out on a spot in the final.
Andino progressed through to today's decider against Hawaii's John John Florence.
"It's one of those situations where if you look at this experience as something that could rattle someone or not, Julian Wilson's experience in Jefferys Bay with Mick Fanning, and Kolohe, this is the third time at Margaret River he has clambered on the back of a ski in this situation," Aussie surf legend Barton Lynch.
"So both of these guys are well experienced with these situations and interruptions. If any two people are going to handle it, it's these two."
The event has been overshadowed by a series of shark sightings.
Surfers were given a scare on Sunday when a shark was sighted near the competition area.
Seth Moniz and Andino were picked up by jet skis midway through their quarter-final showdown after a shark was spotted behind Main Break.
Competition organisers restarted the heat once they had ensured the shark had moved away from the area.
The incident comes just over a year after the 2018 event was cancelled midway through due to two nearby shark attacks on recreational surfers.
Extra safety measures have been implemented for this year's event. Drones have been employed for the first time to monitor shark activity, while the WA Fisheries Department have been dropping an acoustic receiver in the water each day to detect tagged sharks swimming nearby.
The event was moved from mid-April to late May/early June in order to avoid the annual salmon run.